1) Dragon Encounters.
After finishing the main quest,every single time I use fast travel a dragon appears not counting the random dragons and those who guard specific places.
Dragon encounters have become so frequent they are annoying.I can't go anywhere without meeting one,and there were times where I had to fight with 3 of them at the same time!
That basically forces me to abandon this character and start all over again,it isn't nice.

2) The Journal.
Since the journal entries are stored on my pc,or in discs for the console players,and since text display doesn't impact performance WHY every time a quest is updated the text of the former step vanishes??
Why not to be able to read the old text ? For some quests,some journal entries aren't very informative and thus I have active quests that I don't know what they are about because I forgot. In such a big game the journal should be more sofisticated.And the miscellaneous quests.. Are in grave need for text.I mean I have like 40+ active miscellaneous quests but I don't play them.Why ? Becuase how I'm going to get involved enough if I don't have any clues about them at all ? No names of important npcs,no description of what these quets are all about.. I've been playing a month and I can't remember what a random npc I met 2 weeks ago told me along with another 200 npcs I met all that time.
The journal is very lacking,enough to make me loose interest in playing most of the quests.

3)The way the UI works.
The UI is messed up.Not only the keys aren't working properly,but the game doesn't 'remember' keybindings which can lead to situation where it tells me to press [Enter] to save,I press [ENTER] and the wrong action happens instead: the game pauses.Except that, the procedure of finding and selecting an item is longer than ever.In Oblivion with 2 to 3 clicks I could select the item/spell I wanted.In Skyrim it's about 4 to 8.And finally the cross type of it is confusing.
I've completed the main quest and still haven't get used to it,and some times when I'm in the middle of a fight, I want to choose a spell but I end up in the inventory menu,and the opposite.It's confusing and broken.

That's very strange, after finishing the main quest dragon encounters seemed to get less frequent for me - although I'm not sure if this is actually true or just an impression.

I've never had it so a new binding didn't take effect, but in some situations it won't change the keys it tells you to use. For example, I use [tab] as my active key, and E for my character menu key, and [tab] and E are also used in a number of other instances. However when it tells me I can use these keys it displays the default options, and doesn't realize I've switched them, so it tells me to use E to take a book with me even though I actually need to use [tab]. It took a bit to get used to this, although even if it no longer bothers me it would be nice to see it fixed.

I use Esc to exit when I'm gonna exit when I'm buyin things but in right corner it shows Tab to exit.

For me it is the R / F switch.
Morrowind and Oblivion uses "F" to ready weapon and Oblivion uses "R" to change/rotate view.

But since Fallout 3 (yes Skyrim suffers a lot from know Fallout bug ect.)
It had switched, "R" to ready weapon and "F" for the view....

So i changed it back to my trusted Morrowind/Oblivion settings. (I bet i am not the only one how switch it back)
And now i get wrong keybinding for menu, bookshelfs, chests, sacks....... it tells me "R" to drop/store and "F" to favourite but it is switched and have to press "F" to drop/store and "R" favourite.

I think the journal will be the way it is because there are no important NPCs, descriptions, etc for the miscellaneous quests. Skyrim has almost zero directions - it's terrible.
I think some of it is because of Radiant Story, and the other part of it is because of lazy developers.

The journal and quest descriptions and directions makes my rating for this game go down from 9.5 to 8.5 It's THAT bad. Because as you say OP, you end up having so many quests you no longer know what to do with.
The only way is to use Clayrvoience constantly or just follow the marker... without even knowing what you're actually following. How fun is that Bethesda? Please change this for your next game if you read this Bethesda.

Same here.
What's even more annoying is when you get a quest that isn't even radiant and not the slightest hint is given where to go.
They just tell you you have to get xxx (maybe they add from yyy) but there is no way of asking where yyy is over even worse where you are supposed to look for xxx so your only option is to use the questmarker.